similar to: Difference between P.Value and adj.P.Value

Hallo, how can I store a variable as a tab-delimited txt-file? I crated a variable with the following commands: > fit12<-lmFit(qrg[,1:2]) > t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$genes[,1]) > t12 ID logFC t P.Value adj.P.Val B 522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965 1555 CD44_WIZ -6.569622

Hallo, I just made a boxplot with the following command: boxplot(vsnrg$M~col(vsnrg$M)) When I now look at the plot. On the x-axis I just find numbers 1-6 because I have 6 datasets plotted. Now I want to add there the corresponding names which can be found in colnames(qrg). How can I realize this the online help does not help me. Thanks Corinna

Hello, All: I want to simulate future observations from fits to heteroscedastic data. A simple example is as follows: (DF3_2 <- data.frame(y=c(1:3, 10*(1:3)), gp=factor(rep(1:2, e=3)))) # I want to fit 4 models # and simulate future observations from all 4: fit11 <- lm(y~1, DF3_2) fit21 <- lm(y~gp, DF3_2) library(nlme) (fit12 <- lme(y~1, data=DF3_2,

Hi, I wish to analyze with R the results of a perception experiment in which subjects had to recognize each stimulus among three choices (this was a forced-choice design). The experiment runs under two different conditions and the data is like the following: N1 : count of trials in condition 1 p11, p12, p13: proportions of choices 1, 2, and 3 in condition 1 N2 : count of trials in

Thomas B. Ruecker wrote: > Michael Grigoni wrote: > >>Greetings: >> >>It would be nice if Icecast supported RTSP; > > It probably never will > >>however I would >>appreciate any suggestions for a small RTSP/RTP solution to >>encode 8kHz mono audio in GSM or ADPCM and service multiple >>unicast client connections. > > why not use

Dear R-Helpers, I have a data.frame (df) and the head of data.frame looks like ProbeUID ControlType ProbeName GeneName SystematicName 1665 1577 0 pSysX_50_22_1 pSysX_50 pSysX_50 5422 5147 0 pSysX_49_8_1 pSysX_49 pSysX_49 4042 3843 0 pSysX_51_18_1 pSysX_51 pSysX_51 3646 3466 0 sll1514_0_2 sll1514 sll1514

I'm trying to analyze the following data set (sample): "ID" "adj.P.Val" "logFC" "Gene.symbol" "1419156_at" "5.32e-12" "2.6462565" "Sox4" "1433575_at" "5.32e-12" "3.9417089" "Sox4" "1428942_at" "2.64e-11"

Hi, I am really new to edge R and I have used it to calculate gene expression with RNASeq data comparing 2 different conditions. I used a P value of 0.05 and I got a list of DGE contigs up and down regulated. WhatI was wondering is how to convert the logFC value that appear in the output of the exact test. Is it a log2 base? Is fold 2 change considered as cutoff? I am trying to find this info on

hi I have a matrix (10x10) and I have to perform t tests on each row by considering first 5 elements as data set A and next 5 as data set B. This part is easy, However after one t test on each row, I have to randomly permute each column to get new values for each row and then perform another t.test. I can permute the column randomly using the function sample(x) but i am having problem in fitting

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Hi BioC user, I have a problem extracting the gene set I would like to work with. Here is I work with my data: normData <- read.delim("normalizedData.txt",sep ="\t") ######### two class unpaired comparison # y must take values 1,2 classes <- c(-1,-2,1,2) #prepere the data for the samr analysis data.x <-as.matrix(normData[,8:11]) d=list(x=data.x,y=classes,

Hi, just making some experiments with design library i get an error if i want plot(fit) - show below from onlineHelp !? ..perhaps is here another mask problem?, but label from xtable which was my first problem is now off ! Thanks for advance & regards, Christian $ n <- 1000 # define sample size $ set.seed(17) # so can reproduce the results $ age <- rnorm(n, 50, 10)

Hello list. I'm trying to rebuild the 2.6.9.67.0.20.EL kernel, but it fails even without modifications. How did I try it? Created a (non-root) build environment (not a mock ) Installed the kernel.scr.rpm and did a rpmbuild -ba --target=`uname -m` kernel-2.6.spec 2> prep-err.log | tee prep-out.log The build failed at the end: Processing files: kernel-xenU-devel-2.6.9-67.0.20.EL Checking